prophecy child
by Thewolvesaremyfamily
Summary: "you will hand over your child now Doctor or we will kill..." the Doctor and River have a child but danger faces the family as always. what must the Doctor do to protect his family? includes companions from the past. Disclaimer I do not own Doctor who or any of its characters.
1. message

Chapter 1 message

The TARDIS was under attack. The Doctor and River tried to stabilise the TARDIS so they could get away. They got a safe distance away when they received a message. The Doctor opened up the message and it was Madame Kovarian with some silence in the back ground. She said "Doctor you will hand over your child now or we will take your friends. We will take everyone who has ever travelled with you, everyone who knows you and we will kill them" she smiled at the last part. "You have 24 hours to hand her over. See you soon".

The Doctor hit the control panels with anger. River tried to sooth him but he pushed her away. Before they knew it Phoebe was in the room and she said "their going to take me away aren't they?"

River opened her arms and Phoebe ran into them. River stroked her hair as Phoebe cried into her shoulder. She said "no their not going to touch you".

The Doctor looked at his wife and daughter and said "don't worry Phoebe. I have a plan".

As River held Phoebe she looked at the Doctor and said "care to share sweetie"

The Doctor was rushing around to TARDIS as he said "we are going to take Phoebe somewhere safe".

Before he could say anymore Phoebe pulled away from River and as she shook her head she said "No dad. Kovarian came after me when I was a baby and because of that you sent me away for eight years. Dad I don't want to leave you again".

The Doctor embraced Phoebe and said "were not leaving you". The Doctor pulled away and began to steer to TARDIS.

"Then what are you doing?"

The Doctor looked at river and said "River have you ever heard of P.A.L ?"

"No. What is it?"

"P.A.L is a secret organisation that is UNIT and Torchwood. They put their best and brightest into it".

Phoebe looked at her dad and said "what does P.A.L stand for?"

"It means Protect Alien Life."

River walked up to the doctor and said "Doctor how can we trust them?"

He stared into her eyes and said "we can trust them because people who I have travelled with are apart of the organisation".

River nodded and before they knew it they had landed. The Doctor told River and Phoebe to stay in the TARDIS till he told them to come out. River held Phoebe in her arms while the Doctor was walking towards the door.

As the Doctor walked outside he saw some of his closest friends. He saw Captain Jack, Martha and Mickey. He smiled as he saw them and Captain Jack said "you've regenerated again. I liked the other face better".

The Doctor laughed and said "No. I actually like this face better. I can wear a bowtie with this one" as he said bowtie he straightened his.

They all embraced each other then Jack said "so what brings you here Doc?"

He looked to the floor then back up to his friends and said "I'll explain everything later but right now I need you to get everyone down here. Everyone who has travelled with me try and get them down here". They all nodded and went to make phone calls. They all watched as the Doctor went back into the TARDIS and they all had confused looks on their faces.

When the Doctor went back into the TARDIS River was sat on one of the steps and Phoebe was asleep with her head on Rivers lap. He sat down next to them and said "you should get some sleep. We only have a couple of hours".

"A couple of hours till what?"

He kissed her forehead and said "I have just told some people of mine to get everyone down here. They are going to get everyone who knows me down here so we can protect them. When they get here I will introduce you and Phoebe and then the work begins".

River was stroking Phoebes long brown curly hair and said "Doctor I can't lose her again".

The Doctor pulled her close and said "hey were not going to lose her". River had tears falling down her cheeks and the Doctor kissed them away. "I promised you the day we got her back that I would protect her and that is what I am going to do".

They kissed and then Phoebe began to stir. The Doctor picked her up and placed her in her room and he kissed her forehead as he left. The Doctor told River to get some sleep and although she said she was fine the Doctor gave he a look that said go. As soon as River was asleep the Doctor walked outside the TARDIS to see how many people were coming.

Just before he walked out of the TARDIS he wiped away a tear that fell and then opened the door. As soon as he walked out his past companions knew that there was something wrong but didn't ask. He clapped his hands together and said "so who have we got coming then?"

Jack coughed and said "we have Sarah Jane and her team coming down".

Martha said "we have Donna and her husband Shaun".

The Doctor frowned and said "wait Donna she can't remember me".

Jack smiled and said "ow yes she can. A couple of months ago she found me and said that she could remember you and her adventures. But she can't remember all the time lord stuff that was put into her head".

The Doctor nodded and said "who else?"

Mickey turned to him and said "we have a Clara on her way here and she is bringing Angie and Artie".

"Great. Who else?"

Jack looked to the floor and said "Doc that's all we got. Everyone else is rather dead or said if there is danger they would defend themselves".

The Doctor put a hand through his hair and said "that's fine just get everyone here fast".

They all nodded then Martha said "Doctor why don't you go and get some sleep and we'll shout you when they start to arrive".

He shook his head and said "No I have to keep working".

"Doctor" she stared into his eyes "Go. We'll get you when they arrive".

He nodded and said "okay a couple of hours won't hurt".

He walked into the TARDIS but didn't go to bed. He sat by the consol and started to cry into his hands. All he wanted was his family and friends safe and because of one person in the entire universe they couldn't be.


	2. arrival

Chapter 2 Arrival

The Doctor was still sat at the consol when he heard a knock on the door. He walked towards the door and when he opened it he saw Martha and she said "their starting to arrive". He nodded and walked out of the TARDIS.

Martha had empted the room that was around the Tardis so all the companions and friends of the doctor could have room. When he walked out of the Tardis he saw Sarah Jane and her team. They were all sat down on chairs then the Doctor said "hello Sarah".

She turned around then embraced her friend. The doctor then said hello to Luck, Rani, Clyde and Sky. After they said their hellos Clyde said "so Doc what we doing here?"

"I will explain when everyone is here".

Jack, Martha and Mickey walked up to them and Sarah Jane introduced them to the rest of the team. The Doctor was leaning against the TARDIS and was smiling as he saw his friends get to know each other. The door opened and the next person to arrive was Donna and her family. Donna shouted "where the hell is he then?"

The Doctor looked at Donna and said "Hey Donna".

Donna charged towards him and said "YOU".

The Doctor rushed behind Jack and said "Jack whys she angry?"

Jack laughed as Donna tried punching the Doctor. When he was done laughing he said "maybe it's because you wiped her memory".

The Doctor hid behind Shaun and said "Donna listen that was for you own good and...And if I didn't do it you would have never of married Shaun". Donna seemed to calm down and he said "hey Shaun nice to meet you".

Shaun shook his hand and said "yeah you too. Heard a lot of stories can't believe I finally met you".

Donna joined the rest of the group and introduced Shaun to everybody. The last person to arrive was Clara. When she walked through the door and she saw the doctor and she said "Listen I had to lie to their dad. So this better be life or death or it's gonna be".

The Doctor embraced Clara and said "Clara I've missed you".

"Missed you too. So what you been up to, it's been 2 years for me?"

"For me it's been 15 years".

Clara's eyes went wide open and she said "15 years" he nodded and she said "River still got you rapped around her finger".

"She does not have me rapped around her finger".

The Doctor looked to the floor and she said "she's not already is she".

"No, no, no she's alive".

"Then why do you look so unhappy when I said River?"

"I'll explain everything later" She nodded.

The others heard the conversation and Jack said "who's River?"

The Doctor sighed and said "I'll explain to everyone in a moment" he pushed Clara and the kids in front of him and said "this is Artie and Angie. And this is Clara".

Clara smiled and said "hey".

Jack took a step forward and said "hey Captain Jack Harkenss".

"Jack stop it".

Jack rolled his eyes while everyone in the room laughed. After a few moments Martha said "so Doctor why are we all here?"

He sighed and said "I think you should all take a seat" he looked at Donna and Clara and said "Donna, Clara can you come with me?" they nodded and the Doctor took them out of the room.

Everyone in the room had confused looks on their faces.

When the Doctor, Donna and Clara were alone the Doctor said "Donna do you remember when we went to the Library?" she nodded and he continued "the woman who gave her life at the library is apart of my life. We both go in opposite directions. She is in my Tardis alive but I need you to pretend that you don't know how she dies. Pretend that you just met her".

She nodded and said "Doctor I won't tell her but...why would you have her apart of your life when she dies for you?"

He sighed and said "that is what I will explain to everyone else. Just pretend you don't know her".

She nodded and he turned to Clara and said "Clara she's met you but like always pretend you don't know how she dies and be careful what you say about the past and especially don't mention Trenzalore".

She nodded and said "I still get confused with all this River stuff" he gave her a confused look "you know how when I met her at your grave but she only pretended to meet me because she met me before she died". Donna looked at her with wide eyes and Clara said "Believe me River Song is complicated".

They went back into the room and Clara and Donna sat down. The Doctor stood at the front and he said "I have brought you all here today because you are in danger".

Mickey said "what kind of danger?"

"There is an organisation out there who wants me dead".

Sarah Jane said "why?"

"There is a question that will be asked in the future. The oldest question in the universe".

Martha said "what's the question?"

"All of you think what's the first question you ever asked me?"

They were all thinking then Clara said "it's obvious" they all looked at her "I know what the question is so it's obvious to me but it should be to everyone else." She rolled her eyes and said "the question is, Doctor who?"

Clyde looked at the Doctor and said "why would they want to kill you for asking that?"

The Doctor clapped his hands together and said "Because Clyde this question no one will be able to answer except two people in the entire universe. We both know the consequences of saying my name".

Sarah Jane said "Apart from you who's the other person?"

"That who I want you all to meet" as the Doctor walked into the TARDIS, Clara and Donna stared at each other as they knew who he meant.

The Doctor went past the control room and headed for his and Rivers bedroom. When he got there he looked at her sleeping body and sat next to her for a moment. Then he kissed her and said "River its time".

River began to stir and she said "who came?"

As River sat up he said "Sarah Jane and her team. We also have Clara and she brought the children because they have been in the Tardis. We also have Donna and her husband Shaun".

"Wait I thought Donna forgot".

He nodded and said "she did and then she remembered. We also have Martha, Mickey and Captain Jack".

River got dressed and put her gun around her waist and grabbed her blue book just in case she needed it. They went to Phoebe's room to wake her up. While they were in there they noticed that she had been crying again. As Phoebe got dressed and grabbed her purple sonic screwdriver that her dad give her for her birthday, the Doctor and River waited in the control room. When she came into the control room the Doctor told them to wait a moment.

He walked out side and stood at the front again. He then said "The only other person in the universe who knows my name is...my wife River Song".

River heard him say her name and she and Phoebe walked out of the Tardis. As she walked up to the front to meet the Doctor she could see that everyone even Clara had a shock look on their face.


	3. story

Chapter 3 story

As she stood next to the Doctor she couldn't help but smile at the looks on people's faces. The Doctor and River stood next to each other while Phoebe stood in front of them in the middle. The doctor had his arm around Rivers waist then Clara stood up and said "when did you have a kid?"

Martha looked at Clara and said "wait you knew he had a wife?"

Clara looked at Martha and said "yes I've met River but I haven't met the kid".

Everyone in the room kept talking about her and Phoebe rolled her eyes because she was fed up of people talking about her like she wasn't in the room. She got her purple screwdriver and aimed at one of the speakers. The speakers made a loud noise and when it finished Clyde said "what was that for?"

"Because you are all talking about me like I'm not here. Now let my dad talk". She smiled and looked up and the Doctor and he nodded.

Everyone looked towards the front and River and Phoebe sat down at the chairs in front the Doctor. He sighed and then said "okay first is first. Put you hand up if you want to hear the short version or the long version of mine and Rivers life. Put your hands up for Long".

Everyone put their hands up and the Doctor couldn't help but keep on looking around the room. After a few moments Angie said "well aren't you getting on with it then".

He nodded and said "Yes err where to begin...well after I regenerated I found a new companion and her name was Amelia Pond". The Doctor and River looked to the floor for a moment as they tried not to remember Manhattan. "I met her when she was a child and she had a crack in her bedroom wall that was eating away her memories. The crack little did I know at the time, was the end of the universe. I returned when she was older to fix the crack but a prisoner escaped. I saved the world in 20 minuets then I came back a year later".

Luke said "why did you keep on going back?"

"Because I was only meant to be gone 5 minuets when she was little and it turned out to be 12 years. Then when she was older it happened again but I was only gone for a year. Before the prisoner was taken he said `silence will fall'. Me and Amelia who liked to be known as Amy went for a few adventures and we heard that same saying but we never could figure out what it meant. As we travelled we met River a few times and then Amy wanted to go back home. When I took her home she told me that, that was the night before her wedding day".

Jack grinned and said "I bet that didn't turn out well".

The Doctor pulled a face and said "actually she tried to kiss me".

Everyone started to laugh and Donna said "how'd you feel about that River?"

River looked at her with a face and said "believe me its worse than you think".

Jacks eyes widened and he said "Doc continue".

The Doctor clapped his hands together and said "right...I told Rory her fiancée and to make it up to them I took them to Venice. There we battled fish vampires and they spoke of silence falling where they were from. After that we went on a few adventures and Rory died. We noticed that the crack in Amy's wall was following us and when Rory died the light from the crack surrounded him. He was never born. Later me and Amy met River again at the Pandorica".

Jack interrupted and said "wait...the Pandorica isn't a legend?"

The Doctor shook his head and Rani said "what's the Pandorica?"

As Sarah Jane looked at the Doctor she said "the Pandorica is said to hold the most feared being in the entire universe".

The Doctor looked at her and said "and it did. River was there pretending to be Cleopatra so she could hand me a painting by Vincent Van Gogh. She managed to get a complete Roman regiment on her side".

Mickey's eyes were wide open and he said "how did you get them on your side?"

She smiled and said "hallucinogenic lipstick".

The Doctor continued "anyway theirs something I forgot to tell you. Me and River travel in opposite directions...her past is my future so if you here the word spoilers especially from River that is why. Anyway, the Pandorica was at stone hedge and we managed to get inside but when we arrived it started to open. Later we found out that all my enemies were working together to trap me in the Pandorica. River went back to the Romans for help and there she found Rory alive. The entire Pandorica and Romans were from Amy's dreams. When they came Back River went to the TARDIS to get it back to the Pandorica but she was trapped inside. Rory still had all of his memories but Amy didn't remember him until he nearly killed her. He was a robot and my enemies were controlling them to kill everyone. Rory got me out of the Pandorica and we put Amy inside because it forces you to stay alive. Rory waited with Amy for two thousand years and then we set her free. When we set her free the world was falling apart because of the cracks and River was still trapped inside the TARDIS. I managed to get River out of the TARDIS and then I was shot by a Dalek".

Martha said "how many times have you regenerated?"

"Just once you didn't let me finish. When the Dalek shot me it didn't have enough power to kill me but I had to make River, Amy and Rory believe I was dead. I used Rivers vortex manipulator to sneak downstairs to work on a plan. While they were making their way down to me River knew I was lying but she killed the Dalek".

River interrupted "how'd you know about that?"

He gave her a cheeky grin and said "Amy told me word for word what the Dalek said and may I say show-off".

She grinned to him and jack said "what did you say to the Dalek?"

She looked at him and said "the Dalek was going to kill me because it thought that I was just a companion but then I told it to look through its records and I'm sure it found my past because it started to beg for mercy".

Mickey's said "you made a Dalek beg for mercy?" she nodded "Doctor no offence but your wife is more scary then you".

The Doctor and River laughed and Phoebe said "just wait till you hear the end of the story...it gets better".

The Doctor smiled and continued "anyway I told Amy to remember her parents because the crack in her bedroom wall had taken them away. I flew the Pandorica into the heart of the TARDIS and the world went back to normal; but of course I never existed. At Amy's Wedding River gave her, her Blue book which keeps a record of all of our adventures in to make her remember". He glared at River "which I still think was a stupid idea".

She put on an innocent face and said "It brought you back though".

The Doctor sighed "Amy remembered and she brought me back. She gave me Rivers book and I gave it back to her later. After the wedding I took Rory and Amy for a few adventures and I found out along the way that Amy wasn't Amy she was a flesh clone. We found out that she was pregnant and we searched for her. We found out that she was being held at an asteroid called Demons run and I called in a few favours so we could get her; we even asked River but she didn't come for certain circumstances. The baby was named Melody Pond and while we were at Demons rum we found out that she was half human half time lord or in this case time lady. We thought that we had won but there was a battle and we found out that the baby we had was just a clone like Amy was. After the battle was over River showed up and she told us who she really was. Every time I asked in the past she always said spoilers".

He looked at River and nodded for her to continue "Remember when I said before it was worse that Amy kissed the Doctor. I couldn't be at the war because it was about me and if I intervened it would change my future. I couldn't be there because...I am Melody Pond. Amy and Rory are my Parents".

Everyone gasped and Jack said "your a Time lady?" she nodded "wait if Amy and Rory were human how are you a Time Lady?"

"I was conceived in the time vortex and it altered my DNA. The Doctors mistake of having a couple on board the TARDIS".

The Doctor walked up to River, kissed her forehead and said "it wasn't a mistake River you have to stop thinking like that" she looked into his eyes and he went back up to the front to continue. "I searched for River but I could never find her as a child even though she was under Amy's nose the entire time. They took the child away and trained her to kill me" River couldn't look at him it hurt her too much when he talked about this. "Eventually after regenerating a couple of times she found Amy and Rory and grew up with them as their best friend. When River who was known as Mels grew up she found me; when Amy and Rory called. She was running from the police".

Everyone looked at River and she said "technically I was driving not running sweetie".

Clara smiled and said "what did you do that time?"

"I only borrowed a car".

Clara laughed under her breath "your definition of borrowed is not returning the item or asked permission to take it".

"Well it was returned...by the police".

The Doctor clapped his hands and said "well after I had met Mels she held me at gunpoint and we all went into the TARDIS. We ended up going back to World War 2 where we met Hitler. While we were there, there was a teselecta that wanted Hitler to be punished for his crimes but arrived to early in Hitler's time stream. The TARDIS crash landed and we saved Hitler life, but the TARDIS was broken because someone shot it" he glared at River. "Anyway we made our way out of the TARDIS and Hitler tried to shoot the teselecta but he shot Mels instead. At the time we didn't know that Mels was River. After he shot her she regenerated into River".

River interrupted "we need to go back in time and punish Hitler for making me regenerate".

"River he's already dead".

"So he needs more than a punch in the face for shooting me".

Jack said "you punched Hitler?"

"No my dad did".

The Doctor said "okay moving on. We put Hitler in the closet because he was getting in the way. After Mels regenerated into River she tried to kill me and eventually she did. She had poisoned me and she was on the run in Berlin so Amy and Rory went after her. During this time the teselecta noticed River because in her records she is named as the woman who kills the Doctor" everyone stared at River being weary of her. "now after we took down the teselecta I died but then River used all of her remaining regenerations to bring me back to life".

Rani looked at River then said "wait so you killed him and then you saved him". She nodded and Rani said "god your relationship is complicated".

The Doctor continued "we left River at the best hospital in the universe because she had to make her own way to me. Now I took Amy and Rory home because I had some business to take care of and I sent a message to them to meet me at Utah I also sent one to Stormcage for River".

Jack interrupted "wait...you were in Stormcage?"

She had a cheeky grin on her face as she said "yes and by the way it's quit easy to get out of".

Donna looked at Jack and said "what's Stormcage?"

Jack looked around the room and said "Stormcage is a prison in the 51st century that holds the universes most dangerous criminals. It is meant to be the most secure prison in the entire universe, how did you get out?"

River said "Spoilers".

Everyone looked back at the Doctor as he said "told you she does that. Now the next part of the story Phoebe is not allowed to know. So Phoebe and anyone else who is under sixteen wait outside".

Phoebe stood and said "dad that's unfair you never tell me".

"And for good reason. We'll tell you when you're older".

Angie, Artie, Phoebe and Sky were almost out of the room when River said "Phoebe your screwdriver please".

Phoebe walked over to her and said "why do you need my screwdriver? It only opens doors".

River smirked and said "the TARDIS told me what you did to it. Now hand it over".

As she handed to sonic over she said "this is unfair your the daughter of the TARDIS she tells you everything".

Before River could say anything Phoebe stormed out of the room. As River sat back down the Doctor said "what did she do to her sonic?"

"She amplified the sound mechanism so she can hear through walls".

The Doctor smiled and said "clever girl. Well let's get back on with the story. When we all met up at Utah, what they didn't know was that when we faced the teselecta in Berlin I took some information from it. It told me that I will die at Utah".

Clyde said "wait so you know where you were going to die but instead of avoiding it, you went to it. Why?"

"Because my death there was a fixed point in time. While we were there, there was an astronaut that rose from the river and this is where it gets complicated".

Martha said "how can it get anymore complicated?"

"Believe me it can. Now there are two versions of this story. Version one the astronaut killed me straight away...version 2 the astronaut created a paradox where history was overlapping".

Jack said "who is this astronaut?"

There were a few moments of silence then River said "me...I was the astronaut. The version of me that the Doctor called was still in Stormcage and the version that was in the suit was before Stormcage. I was placed in the suit by a woman called Madame Kovarian and she was the same woman who trained me to kill the Doctor".

There was silence again then the Doctor said "now River was meant to kill me but she was too stubborn and used up all her power. When we were in the Paradox only a few noticed that time had stopped and Amy created an organisation to try and save me. While we were in the Paradox Madame Kovarian remembered she was apart of the Silence. The Silence isn't a species it's a religious order that want me dead because of the question. The Silence uses these creatures that when you look at them you remember everything about them but when you look away you don't remember a thing. I and River were the opposite ends of the destructor polls so when we got married on top of the pyramid she then killed me".

Rani smiled and said "aww that is so romantic you got married on a pyramid".

The Doctor and River smiled but then Jack said "did anyone else not hear that she killed him afterwards".

River looked at Jack and said "I didn't kill him though. He was inside a teselecta suit so when I shot him he didn't die...but I still went to prison for killing the Doctor".

The Doctor took a step forward and said "well you had to River; the universe had to believe I was dead. Plus you got pardoned anyway".

Luke said "how did you get pardoned for killing the Doctor?"

River looked at him and said "Clara over there wiped all the records of the Doctor so it looked like he never existed. I was in jail for killing a man who didn't exist so they let me go".

Clara looked at River then said "how did you know I wiped the records?"

"The Doctor told me".

Clara glared at the Doctor then said "I thought all of that was a spoiler to River".

He ran a hand through his hair and said "it is, well it isn't. River can know certain parts of the story but she can't know how you got there? Or how you did it?"

River looked between them both and said "which brings me to this, am I ever going to find out?"

The Doctor and Clara looked at each other and both said "Spoilers" at the same time. They couldn't reveal Trenzalore because if they did then they would have to tell her that she died in the library. River rolled her eyes and put them back on the Doctor.

The Doctor said "after the Paradox River went to Stormcage while I, Amy and Rory went on a few adventures. We met with River a few times and the first time we met her when she was pardoned was in Manhattan". The Doctor and River both have tears in their eyes then he says "while we were in Manhattan we lost Amy and Rory. The weeping angels sent them back in time and we couldn't go back to get them; their time is sealed to us".

Everyone looked at The Doctor and River and could see that it hurt them to talk about it.

The Doctor continued "after that River went back to teach at the University and I travelled with Clara". The Doctor looked at Clara and even she was upset by the story. Clara had been there throughout his life and saw what happened to the Ponds. "After Clara left, me and River had Phoebe but we got separated. Madame Kovarian found out about her and tried to take her away. We left Phoebe for eight years on earth so she was safe. We came back to get her and we travelled for a few years but then Madame Kovarian came back. Early this morning we got this message".

The Doctor pointed his sonic at the TARDIS and it projected the message for him. Everyone in the room had shocked looks on their faces when Kovarian demanded Phoebe or she would kill everyone.

When the projector went off and Sarah Jane said "why do they want her?"

"They want her because she is more Time Lady than River is and they think she will be stronger if they train her to kill me".

Martha looked at the Doctor and said "but she's a teenager now. She knows who you are and what you have done. Wouldn't it be harder to train her"?

The Doctor shook his head and said "no it wouldn't be. They know that if they got their hands on Phoebe I would die to get her back, which is exactly what they want".

Jack stood up and said "so we stop them before they can hurt anyone. We protect ourselves and we protect Phoebe".

"Jack I don't want you guys involved".

"Were already involved Doc. I say if we do this right we can come out of this alive. We do this together".

The Doctor didn't argue and one by one everyone in the room stood up and said "together".

A few minuets later the children came back in and they told them that they were all going to stick together. After a few moments of everyone feeling safe a sudden burst of light was in the room and you could make out some figures. River and the Doctor were frozen and Phoebe said "mum, dad is that-?"

Before she could finish the Doctor said "yes it is".

**AN: I know this chapter is longer than the others I just wanted to put all the story of the Doctor and River together in one chapter. **


	4. enemy or friend

Chapter 4 enemy or friend

Everyone was stood in front of the light as it cleared and the Figure was more noticeable before anyone could speak the woman in the light said "Melody Pond what have you done now?"

The Doctor and River were shocked as they saw Amy and Rory walk out of the light. Amy and Rory walked up to River and Rory said "River what's going on?"

She was in shock and she just whispered "mum...dad" before anyone else could speak Amy had her arms wrapped around River with a smile that went from ear to ear.

When they pulled away Rory embraced River and Amy walked up to the Doctor. For once the Doctor was speechless and Amy couldn't help but laugh at the look on his face. When she stopped laughing she said "well are you just going to stand there like a statue?"

She wrapped her arms around him and when they parted the Doctor said "how can you be here?"

"Ask them". She directed her look towards the light and as it closed, out came Madame Vastra, Jenny and Strax.

When everyone could see them Luke picked up a chair and shouted "Sontaran".

As Luke ran towards Strax the Doctor stepped in front of him and said "Luke put the chair down he won't kill us. He's an old...friend." Luke put the chair down but everyone was still on red alert.

When everyone calmed down River holding Amy's hand walked up to Madame Vastra and said "Madame Vastra what are you doing here?"

"I was about to ask you, what is going on?"

The Doctor looked at her and said "what do you mean?"

"Back in our time we have just had silence in our home. We knew that something must be happening for them to come for us so we went to Amy's time" she gestured to Amy "which by the way is hard to get to. We located you here to find out what's going on".

River looked at the Doctor and said "I thought they gave us 24 hours".

He said "clearly they know what were up to".

Amy had confused look on her face and she said "24 hour till what?" River went to stand next to the Doctor and she told Phoebe to stand by her side. Amy noticed some similarities between the child and River but couldn't put her finger on it. She looked at River and said "River who's the kid?"

River moved Phoebe forward and said "this is mine and the Doctors daughter. This is Phoebe Amelia Song".

Amy moved closer to Phoebe and said with a smile on her face "This is my Granddaughter". River nodded and as Amy embraced Phoebe. When she pulled away her smile had faded and she said "this is my Granddaughter".

River looked at Rory then said "Father I think mum is going to faint".

After Amy had got over the shock of having a granddaughter the Doctor said "so Ponds let me introduce you to some people". He turned them around so they could see his past companions and friends. He pointed to each person and he said "that is Sarah Jane smith and her kids Luke and Sky smith. These are their friends Rani and Clyde and they protect the world from an attic in London. This is Artie and Angie and Clara the impossible girl".

Before the Doctor could move her along she said "why are you impossible?"

Clara just looked at the Doctor because she didn't know what to say. The Doctor said "she's Impossible because she keeps on popping up all over history" before Amy could ask what he meant he moved her along. "This is Donna and he husband Shaun. This is Mickey, Martha and-"

He was interrupted by Jack saying "hey I'm Captain Jack Harkenss".

The Doctor made a face and said "Jack stop it she's married".

While everyone was getting to know each other the Doctor and River stood towards the side as they watched their family and friends get to know each other. River had her head leaning on the Doctors shoulders as he had his arm wrapped around her waist. He couldn't help but over hear a conversation Jenny and Madame Vastra were having. Jenny said "do you think it is the child from the prophesies?"

Madame Vastra was paying close attention to Phoebe and then she said "I don't know she could be".

"Being the Doctor and Rivers Daughter would make sense. They are feared through out the universe".

"Yes I know. Jenny listen we must keep this quiet, just until we know for certain". Madame Vastra looked at the Doctor. He looked at her with a worried look as he didn't know of the prophecies.

When everyone was finished talking Amy turned to the Doctor and said "so you said they gave you 24 hours. 24 hours till what? And why is everyone gathered here?"

Everyone looked at the Doctor and River. They both looked at each other and wondered how Amy would react. River took a step forward and wrapped her arms around phoebe then said "Doctor Play the message".

The Doctor sonic the TARDIS to play the message while Phoebe and River looked away. When Madame Kovarian showed up with her eye patch on and silence in the background Amy's heart skipped a beat. When the message was finished Amy had tears in her eyes but didn't let them fall. She walked over to River then Phoebe went to the Doctor and embraced him. While Phoebe was with the Doctor Amy had grabbed Rivers hand and pulled her into the TARDIS.

When they were in the TARDIS Amy embraced River and River let the tears fall. When they pulled away Amy said "River don't worry they wont take her. I won't let them".

"Mother you cant be sure of that. They took me when I was baby".

Amy wiped away a tear that was on Rivers cheek and said "Melody listen. Phoebe is yours and the Doctors daughter which means she is stubborn, smart, brilliant, loved...and most of all she is protected. Kovarian won't get her hands on Phoebe and this time is different. This time Phoebe is older than you were and this time we know all of Kovarian's tricks".

They both smiled then embraced each other once again.


	5. Prophecy

Chapter 5 Prophecy

Outside the TARDIS Rory walks over to Phoebe and the Doctor and without saying a word he embraces Phoebe. The Doctor walked over to Madame Vastra and says "what prophecies?"

Madame Vatra says "Doctor we don't know if she is the" he interrupted.

"Just tell me. If it concerns my daughter then you need to tell me".

Everyone in the room heard the Doctor and turned to him and Madame Vatra and even Phoebe had a concerned look on her face. Madame Vastra knew that she couldn't keep this quiet so she said "okay I will tell you...but not without River".

As if on cue River and Amy came out of the TARDIS and everyone stared at them. They both froze when they walk out and they looked at everyone while River says "what's wrong?"

The Doctors look turns from River to Madame Vastra and says "tell us now".

River narrowed her eyes and said "tell us what?"

River and Amy walked towards the Doctor as he said "there's a prophesy about our child and Madame Vastra here is going to tell us".

Amy was stood with Rory and Phoebe, while River was stood next to Doctor and Madame Vastra narrowed her and said "Doctor we cant tell you here".

"Why?"

Madame Vastra sighed and Jenny could tell that she was fed up. After a few moments of silence Jenny said "if we tell you here then you are in more danger than you are now".

River and the Doctor both had worried looks on their faces and River said "how can anything be worse than this?"

Madame Vastra said "trust us it can".

The Doctor took a step forward and said "you need to tell us".

She sighed then said "we will tell you but not here" she looked at Jenny and said "get the candle".

Jenny nodded and then started too search through her bag. Seconds later she brought a candle out and passed it to Madame Vastra and passed everyone else in the room masks to wear.

Clyde then said "why do we need masks?"

Madame Vastra says "the chemicals in the candle shut down some of the senses to the brain"

He gave Madame Vastra a weird look then said "basically the mask knocks you unconscious" Clyde didn't have to be told twice as he tried to put the mask on as fast a possible. Everyone put on masks except Strax who put on his helmet and said the fumes couldn't get him. They all watched as the Doctor, River, Amy, Rory, Jenny and Madame Vatra sat in a circle. Madame Vastra lit the candle and one by one they fell unconscious. The Doctor quickly glanced at Phoebe who was stood next to Clara before everything went dark.

When they all woke up in a room Amy said "where are we?"

Jenny said "you're exactly where you were before but your just sleeping".

The Doctor then said "you can explain how this place works later. Now Madame Vastra tell me about this prophecy".

She sighed then showed them a picture of an old man in a ball of light. She then said "this is Adam Burnley. 5 years ago in my time he came out of no where and insisted that he was taken by aliens. Because of this he was put in an institution for the insane".

Amy said "was he really taken by Aliens?"

Madame Vastra nodded then said "while he was in the institution I visited him and on the day of his death he told me a prophecy that he heard. At first we thought nothing of the prophecy until me and Strax started to look at the history of our people and in every chronicle we found talks of the prophecy".

River narrowed her eyes and said "how far back does this prophecy go?"

Madame Vastra shook her head and said "we don't know. We've tried to locate when it was created but we have a suspicion that it was made a beginning of time".

The Doctor scoffed and then said "if it was made then I would have heard about it" he stood up and started to walk around the room.

Madame Vastra smiled then said "Melody and Oncoming Storm" he turned around and then she said "now I've got your attention" he sat back down.

He then said "that's a child's lullaby it means nothing".

She laughed then said "you still haven't connected the dots yet have you" he gave her a confused look then she said "You already know that you are the oncoming storm and Rivers real name is Melody. The prophecy has been lost through time and on some worlds it has been made into a lullaby that is until Adam Burnley".

Rory then said "so wherever he was taken to he found out the true prophecy".

She nodded then said "that is correct".

The Doctor then said "what is the prophecy?"

Madame Vastra waved her hand and the image in the ball of light changed. It changed to Adam in his cell and he was telling Madame Vastra the Prophecy. _He said "it is coming"._

_Madame Vastra tried to calm him "Adam who is coming?"_

"_The prophecy will come true"._

"_Adam tell me the prophecy"._

_He calmed down as his breath began to leave him then he looked up at the ceiling and said "the prophecy goes; Darkness comes Darkness will fall. Her parents are feared but she will save us all. To one parent their home is lost but to another their home is earth. She is the child of two worlds and when she saves us she will bring the light to the dark. The child's bravery will come at a great cost, a cost that she will not be prepared for. The child is the child of Melody and the Oncoming Storm" he then looked at Madame Vastra and said "this is the true prophecy. Others have been toyed with and are not true. People will hurt the child before her time is right, her parents enemies will be victorious if she fails. No one must know until the time is right" he then took his last breath._

Madame Vastra moved the image from the ball of light then said "now you know".


	6. reaction

Chapter 6 reaction

Everyone who was conscious was concerned about why the prophecy was so secret that they couldn't know. After the Doctor and everyone fell unconscious Phoebe walked towards the group of people and took her mask off. Everyone stepped forward to try and stop her but before they could she fell. Everyone rushed over to her and Martha got to mask and put it on her face. Clara shook her head and said "putting the mask on now wont work".

Jack said "then how do we wake her up?"

Strax stepped up and said "you can't fool".

Jack stepped up to him and said "and why's that potato head?"

The kids laughed but then Clara stood in between them and said "the Doctor doesn't want this arguing" they both stepped away from each other then Clara said "she can't wake up because it is her choice. She has to wake herself up while she is in that trance" they all just stared at Phoebe.

Inside the trance Phoebe had arrived just as Madame Vastra mentioned Adam Burnley. Phoebe hid behind a wall and she could hear everything and there was a small hole in the wall so she could see the images Madame Vastra were showing. When the finished telling the prophecy Phoebe had tears in her eyes and then a sob escaped her mouth. The Doctor quickly rushed out of his seat and looked behind the wall and saw Phoebe. She stepped away from him and shook her head and then she disappeared; she woke up.

Phoebe quickly shot up and started to cry then the Doctor and everyone else became conscious. River said "Phoebe" but before she could say anything else Phoebe jumped up and ran to the door. The Doctor ran after her and grabbed her hand before she could leave. He held both her arms but she tried to push him away. She was crying hysterically but she calmed down when he said her name. "Phoebe, Phoebe listen to me everything is going to be okay".

She stared into his eyes and said "how dad? You heard the prophecy if I fail your enemies will be victorious. I don't want this prophecy".

He brushed her hair away from her face and said "you don't have to. Prophecy doesn't control you".

"Only if that was true, I can't escape this".

He nodded and said "yes you can".

She shook her head "no I can't. The prophecy has been made into lullabies, Fairytales; it is in every chronicle and was made at the beginning of time". He pulled her into an embrace and she cried into his shoulder and said "Dad, I'm scared".

River appeared besides them and said "your our daughter, you can do anything".

Phoebe pulled away from the Doctor and embraced her mother. River sent a worrying look to the Doctor as they both were as scared as their daughter. When they pulled away Phoebe said "do you think Kovarian knows?"

"Of course I know". Everyone turned around and looked towards the wall. The projector was turned on and Kovarian was there. She smirked and said "we can hack into anything".

The Doctor took a step away from River and Phoebe and said "what do you want?"

"I think we have already established what I want" she looks at Phoebe.

River stands next to the Doctor and says "and we have already established that, that will be a cold day in hell when you get Phoebe".

She laughs then says "then hell will soon freeze over" she then sighed and said "of course we know about the prophecy. She was one of the reasons you had to die Doctor".

River narrowed her eyes and said "if you knew about the prophecy why not kill me when I was a child".

Kovarian was silent but then Clara laughed and said "she didn't know".

Kovarian looked at the group of people stood behind the Doctor and glared at Clara. After what Clara said the whole group were smiling. Angie said "I take it that's the old crone that's causing all the trouble?"

Kovarian's mouth went wide open and everyone laughed and Jack high fived Angie and said "good one kid".

Kovarian glared at each and every one of them and then said "you think you are all safe with the Doctor, you are sadly wrong. I have got people from the Doctor before and I will again. Isn't that right Amelia".

Amy glared at her and said "you stay the hell away from my family".

She laughed and then said "you know me that will never happen".

The Doctor looked at Amy and said "Amy Look at your arm" Amy, Rory, the Doctor and River all looked at their arms. The Doctor then whispered "silence".

They all backed up towards the group of companions and Kovarian says "you think they wouldn't come".

The silence then appeared and Donna said "what are they?"

River pulls out her gun and says "the creatures that work for the silence".

Amy then says "keep an eye on them or you'll forget".

"Doctor, how many?"

The Doctor counted all the silence then said "12".

"okay. Doctor you and Phoebe get the electric off before they" the silence started to pull power from the room "doesn't matter".

Everyone went for cover except River and Jack who were shooting silence and Phoebe and the Doctor who were using their Sonics to help with the power. By the time they fixed the power problem River and Jack had nearly finished taking out all the silence.

Jack had taken down four while River took down eight. Jack stared at her in wonder and said "we could be so good together".

She laughs then says "you know I'm taken".

Everyone came out and then Mickey says "Doctor, how is it you hate guns and yet you have a wife that is".

He tries to think of a word to describe River with a gun but then Clyde says "awesome".

"Yes awesome with a gun".

The Doctor shrugs and says "well...it's...its River"

Amy says "he actually likes River having a gun".

Everyone laughs as the Doctor blushes and walks back to the screen. He then says "did you think that would work Kovarian?"

She smiles and says "of course not Doctor, that's what plan B, is for" she grabs something from the side of her and brings it in the view of the camera.

"No" the Doctor whispers. Kovarian has an arm around a young woman with blond hair and who's in cuffs. She tries getting away but then Kovarian clicks her fingers and two silences come up from behind the woman and hold her.

Kovarian smirks at the Doctors reaction and knew he would be this way. She then said "looks like you can't protect everyone who knows you".

**AN: I know I haven't updated in a while and I hope you accept my apology. I have been having writers block with this story so if anyone has any ideas don't be afraid to pm me. Most of you can probably guess who the blond is but leave a review of who you think it is. **


	7. another

Chapter 7 Another

"_Looks like you can't protect everyone you know"._

The Doctor gritted his teeth and said "what do you want with her?"

Kovarian laughed and said "nothings more powerful than a love for a daughter".

The Doctor started to breathe heavy and River and Phoebe were at either side of him and Phoebe said "sis".

Jenny gave her a smile then said "it's alright sis, I'll be alright".

Phoebe had tears in her eyes as did the Doctor and River. Jack said "you had another kid?"

None of them answered but Martha whispered "she's meant to be dead". They all looked at the Doctor and they felt sorry for him. To protect one daughter the other daughter is endangered.

The Doctor could only stare at Jenny and then she smiled and said "dad Just thought I'd say I'm sorry".

He shook his head and said "sorry for what?"

He narrowed his eyes and then she said "this" the hand cuffs came off her and she grabs a gun from her waist and she shoots the silence. Kovarian's grabs a gun from the side of her and shoots Jenny. The image fades and leaves everybody shouting Jenny.

Before anyone speaks the Doctor Sonics the projector to get the image back but it doesn't work. Then a beam of light enters the room and when everyone looks they see Jenny. She has a hand to her side and she looks at the Doctor and says "hey dad".

She then collapses forward. The Doctor quickly rushes over to her and manages to get to her in time to catch her. She's breathing heavy and the Doctor says "how are you here?"

She smiles and says "a story for another time" she then holds up her hand that's covered in blood and it started to cover with a bright light.

River and Phoebe kneels down beside her and has tears in their eyes. Jenny puts a hand on Phoebe's cheek and says "it'll be alright sis".

"How do you know that?"

She laughs then says "because I'm apart of this family" she then looks at River and says "hey mum".

She smiles and says "hey darling".

She then winced in pain and says "everybody get back".

The Doctor grabs River and Phoebe and runs to the rest of the group. They all watch as Jenny stood up and started to regenerate. Bright light went all over her body and the light was all across the room.

When the light disappeared Phoebe ran to Jenny and embraced her. River then joined them and then they looked at the rest of the group. Everyone looked calm apart from the Doctor, Martha and Donna who had their mouths wide open in shock. Jenny laughed under her breath and said "mum, why does dad looked like he's gonna pass out?"

She sighed and said "do you remember that time we talked about how you father knew you were alive before you met him again?" she nodded "I pretty sure this is the time he finds out".

She smiles at him and says "I'm alive".

"I can see that" he then looks at his wife and Phoebe and says "wait, how is it you know her? Phoebe is always on the TARDIS with me"

Phoebe was silent and looked at River until she said "not always. That exhibition I took her to a couple of months ago...it wasn't really an expedition. I was taking her to meet Jenny".

"Then how did you know her?"

"Sweetie I'm from your future remember".

"Why didn't you tell me she was alive?"

Jenny stepped forward and said "dad, it's not mums fault".

"Mum? Why do you call her that?"

She opened her eyes wide then looked at River and back to the Doctor and said "Spoilers".

"Can you at least tell me how you're still alive?"

She sighed and said "okay. All I know is that after you left and they were giving me a burial I breathed this light out of me. Later I discovered it was regeneration energy but because I'm not really a time lord it took a while to work the first time. After that I travelled a bit then" she stopped.

He narrowed his eyes and said "then what?"

"The rest of that is spoilers".

The Doctor looked at River and said "River".

River grinned as she shrugged and said "sorry sweetie but we taught her well".

As jenny stood next to River, Jack took a step forward and said "if she regenerated then how is she still her?"

The Doctor looked like he was going to answer but then he looked at his daughters and Rivera and River said "we don't know. We never figured it out even in the future. All we know is that when she regerates she heals but she also becomes younger".

Jenny smiles but then she says "why is everyone staring at me?"

The group still had shocked faces and Phoebe says "they did the exact same thing to me".

"But I know most" River interrupted.

"Spoilers".

She gave her an apologetic look and then said "so who knows me and who doesn't?" she looked around the group and says "well Martha and Donna know me that's no spoiler".

Martha and Donna walk away from their husbands with smiles on their faces and embraced her. When they pulled away and said how much they missed her River took Jenny by the hand and led her to the group. She said "this is Sarah Jane Smith".

"She travelled with dad in his third and fourth regeneration and saw him again in his tenth" they all stared at her and she said "sorry my head is full of facts on everyone".

Everyone smiled then Sarah Jane and Jenny shook hands and Sarah Jane said "these are my children Sky and Luke and friends of ours Rani and Clyde".

They all shook hands and they moved on. River then said "this is Shaun, Donna's husband".

As they shook hands Jenny looked at Donna and said "at least this one didn't plot to kill you with a giant spider".

"OY".

Jenny laughed slightly then moved on. "This is Angie, Artie and Clara".

Jenny smiled and said "the impossible girl".

Clara laughed but then River narrowed her eyes and said "how do you know about that? Am I the only one who doesn't know?"

She shrugged and said "sorry mum but it's a spoiler".

River sighed but then Clara said "trust us River you don't want to know why I have that name".

River stared at Clara but then Jenny pushed her along and said "come on mum".

"This is Mickey, Martha's husband and Captain Jack Harkness".

Jack takes a hold a Jenny hand, kisses it and says "hello there".

The Doctor shouted "Jack".

"sorry".

Jack gives her a cheeky grin and she says "I wouldn't Jack if you know whats good for you".

"I'm not afraid of him".

River grinned and said "she was talking about me".

Jenny pulled her along and said "come on we don't want what happened with Jake to happen again".

The Doctor narrowed his eyes and said "who's Jake and what happened to him?"

"He was my ex boyfriend and mum shot him".

The Doctor opened his eyes wide and he said "River".

She shrugged and said "I don't class that as a spoiler. Besides no one liked him. I didn't like him, you won't like him, Phoebe won't like him, even the TARDIS in my time tried to throw him into the sun". The Doctor laughed "he simply wasn't good enough for her".

Jenny rolled her eyes and said "come on mum".

They faced the next group and she said "this is Madame Vastra, Strax and Jenny".

Both Jenny's laughed and then the Doctors Jenny said "from now on everyone call me Jen" everyone nodded and then they moved along.

River squeezed Jen's hand and said "Jen, this is Amy and Rory".

Jen smiled and then said "Amy and Rory travelled in the beginning with the eleventh Doctor and Amy met him when she was" Jen stopped and then glanced between the couple and River and she said "do you mean Amy and Rory? As in thee Amy and Rory, crack in my bedroom wall; recreate the universe, made of plastic, Rory the roman Amy and Rory".

River laughed and said "yes".

Jen had a massive smile on her face and embraced them both which knocked them both back a bit and said "you have no idea how long I have waited to meet".

Amy said "thank you" awkwardly.

When Jenny finally stopped talking about how she heard every story and made her way back to the Doctor and Phoebe, River had the strangest feeling something was off. The TARDIS made a noise and as everyone looked towards it, River said "Jen, how exactly did Kovarian catch you?"

Jen has her hand behind her back and Jack laughed and said "she has a vortex manipulator".

River walked towards Jen and pulled the arm from her back. She said "how did you get one of them?"

Jen laughed and said "spoilers".

River shook her head and said "were on the same timeline. You can't use that excuse with me".

As River let go of Jen's hand Jen sighed and said "I got it from Dorium".

Phoebe narrowed her eyes and said "isn't he headless?"

Jen shrugged and said "you got a lot to learn sis. He might be headless but because of the monks he can still pass along information...if you have the right word".

Phoebe smiled and said "what's the word?"

"All you have to say is".

River covered Jen's mouth and said "Phoebe doesn't need the word because she is making no deals with Dorium". River moved her hand and both the girls sighed. The TARDIS then made a noise and River said "even the TARDIS agrees".

Jen said "that's because you're the child of the TARDIS. She tells you everything what we do". Phoebe nodded in agreement and then Jen quickly said "tell Dorium you're the Doctors daughter".

As River tried to stop her, she sighed in frustration and Phoebe said "thanks sis".

**AN: for those of you who thought it was Rose did you really forget about Jenny. If any of you are confused about the storyline or anything else then please PM me. Just thought you should know I don't know when I will update next. School just started and as most of you know they don't care if you have fanfiction they still set tones of homework. Sorry if I update really late. **


	8. secret door

Chapter 8 secret door

After all the introductions had been made the Doctor advised that everyone get inside the TARDIS. As they all walked inside, except from The Doctor, Jenny, Phoebe, River and Clara everyone else looked around and commented on how the TARDIS design had changed. This was the first time that Shaun and Sky were on the TARDIS and from the Doctors point of view they were taking it pretty well. Donna had hold of Shaun's hand and said "are you alright?"

He looked around and said "you weren't kidding when you said it was bigger on the inside".

Everyone in the Tardis laughed and Donna said to the Doctor "no wonda you like it when people say that".

As everyone made there way to the controls the Doctor was rushing around like the mad man he is. Suddenly there were bright lights all around the TARDIS and Amy said "River, he's doing it again".

Martha said "doing what?"

River stepped to the controls and said "he's attempting to make the TARDIS invisible".

The Doctor rushed towards where River was and said "what are you doing?"

"Fixing your mistakes" after a few clicks of buttons she said "all done".

The lights dimmed and the Doctor said "I know how to work my own TARDIS".

River grinned and said "if you did sweetie then she wouldn't always disagree with you" the TARDIS made a noise "see she agrees with me".

The Doctor opened then closed his mouth and sighed in defeat. He clicked a few buttons and said "all your rooms are that way". As Rani, Sky, Clyde, Luke, Angie and Artie left the room everyone else stood still and stared at the Doctor. The Doctor looked at the people left and said "aren't you going?"

Jack steps forward and says "not until you tell us about this prophecy".

The Doctor looked towards Phoebe and she nods "the prophecy says" all the kids ran back into the control room and started shouting all at once.

They all said "have you seen these rooms", "pool table", "X-box 360", "trampoline".

Eventually Clara and Sarah Jane shouted for their kids to be quite. They all looked to the Doctor and he said "Madame Vastra over here" he gestured to Madame Vastra "met a man called Adam Burnley and he told her the true prophecy. He said "the prophecy goes; Darkness comes Darkness will fall. Her parents are feared but she will save us all. To one parent their home is lost but to another their home is earth. She is the child of two worlds and when she saves us she will bring the light to the dark. The child's bravery will come at a great cost, a cost that she will not be prepared for. The child is the child of Melody and the Oncoming Storm. This is the true prophecy. Others have been toyed with and are not true. People will hurt the child before her time is right, her parents enemies will be victorious if she fails. No one must know until the time is right".

They all looked at Phoebe and she had tears in her eyes again. Jen wrapped her arms around her and whispered comforting words in her ear. Jack was still staring at her and said "that is some destiny".

She moved out of Jen's arms and said "I'm going to the shooting range".

The Doctor didn't realise what she said till people stared at him and said "shooting range?"

He saw as Phoebe placed her hand on a bare TARDIS wall and all of a sudden it opened up and a door appeared. He looked around the room and Jen said "I'll talk to her" she ran off into the door before it closed.

The Doctor looked at River and said "when did we get a shooting range?"

She shrugged and said "it's always been apart of the TARDIS sweetie. You just tend not to look for things like that" she walked off in the same direction as her two daughters and re-opened the door.

The Doctor looked at everyone who remained and said "what?"

Donna shook her head and said "you utter idiot".

He shrugged and said "what did I do?"

"Think about it space man".

He sighed and then Clara said "what do you mean a cost she is not prepared for?"

He shrugged but didn't say anything. Amy said "that is what she is scared off. She is thinking the worst and every time she hears the prophecy...she imagines the worst".

"aww" they all looked towards the door and could see Angie with her hand on the wall. She pulled it away and said "why can't I get in?"

The Doctor looked towards the screen and he said "it's a restricted area. Wait we don't have restricted areas" he looked up to the TARDIS and said "TARDIS, who restricted it?" the TARDIS made a noise and the Doctor looked at the Computer screen and said "restricted, only blood relatives aloud" he sighed and said "thanks".

He sat down and everyone stared at him. He sighed and then Madame Vastra said "Doctor, what is your plan?"

He shook his head and said "I don't know".

"Well we need a place to hide until you can figure one out".

Sarah Jane stepped forward and said "someplace on earth" they all gave her a weird look and she said "Rani and Clyde are restricted to earth by the Judoon".

They all looked at them and Clyde said "It wasn't our fault...really it was all his" he pointed to Luke.

"me? How was it my fault?"

He shrugged and said "if you got the prisoner faster it would have never of happened".

The Doctor said "I'm sorry what exactly happened".

Rani took a step forward and said "basically a Juddon fell the earth with a prisoner. We tried to help him but little did we know the prisoner was the destroyer of worlds and could go into people's bodies. He went into Sarah Jane's and the Judoon wanted to kill her to kill the beast. I and Clyde locked the Juddon into a science lab and we managed to get the prisoner out of Sarah Jane before more Judoon came".

He stared at Sarah Jane wide eyed and said "what do you do on earth?"

She shrugged and said "whatever torchwood doesn't do" she smiled at Jack.

The Doctor looked at Jack and said "that's it. We need a place to think, a place that's safe. How safe is torchwood?"

He said "completely safe, why?"

"Because that's where were going". The Doctor rushed around the TARDIS pressing all the control when the rest of his family came back in fromt he shooting range.

Jen said "dad, where are we going?"

"Torchwood".

The girls rushed around the controls making the TARDIS stable and the Doctor glared at his wife and she said "they learned from the best". They all rushed towards the door and opened it up to find that they were inside Torchwood hub 3.

**AN: I am so sorry for the late update. School work has been getting to me and I lost inspiration for this story and I truly don't know where it is going. If you have any ideas of where you want it to go, please don't hesitate to say. Please review.**


	9. Letter

Chapter 9 Letter

Before the Doctor or anyone else could walk out of the TARDIS guns were pointed at them. The Doctor held up his hands as the gun got closer and took a step out of the TARDIS. He looked at the woman holding a gun and said "Gwen, please put the gun down".

She looked at Rex beside her and then looked back to the Doctor "how do you know who I am? Where is the Doctor?"

People started to walk out of the TARDIS and put their hands up as soon as they saw the guns. When Jack came out of the TARDIS he said "what the hell are you doing?"

They both put the guns down and Rex said "Jack, what are you doing here? You're meant to be at P.A.L".

"Yeah well the Doctor decided to make an appearance and now we need to fight some aliens".

Gwen looked at the Doctor and said "The Doctor?"

He nodded and said "the one and only, well unless there's two of me then were in" he was cut off by a slap from Gwen.

Everyone rushed towards the Doctor and Rex pulled Gwen away and said "what the hell are you doing?"

"What does it look like?"

"You can't kill him till he fixes me".

The Doctor gave them a weird look "okay I don't know what I did to deserve that. 1 what was that for? And 2 what needs fixing?"

Gwen glared at him and said "because you weren't here for Miracle day or when the 4.5.6 attacked".

He stepped closer and said "what happened?"

Gwen looked around and said "no one told him" they all put their heads down "the 4.5.6 attacked 3 years ago. They came here and wanted 10% of the children of the world".

Jack stormed off and the Doctor said "what's wrong with him?"

Gwen scoffed and said "when they attacked Ianto died because the 4.5.6 poised a building he was in. Jack also had to sacrifice his own grandchild to save the children".

The Doctor had tears in his eyes; he shook his head and said "what happened on Miracle day?"

Rex took a step forward and said "that was just under a year ago. The entire world became immortal while jack became mortal once again. People tried killing jack for some reason, so we switched blood so he became immortal. When the world returned to normal he went back to being immortal but I also stayed immortal".

"That's impossible".

After half an hour of explaining to the Doctor everything he missed he decided that he needed to talk to Jack. Gwen and Rex ordered pizza and everyone down stairs was enjoying it and was sharing old stories of the Doctor. The Doctor knocked on Jacks office and then walked in. He saw that Jack had his face in the palms of his hands on the desk and he said "Jack".

He quickly lifted his head off the desk and whipped away the tears and smiled "Doc, lets get back to everyone".

The Doctor stood in front of the door and said "why didn't you tell me?"

"Tell you what?"

"About your grandson and Ianto".

Jack looked down and said "it's all in the past".

"Jack".

"I don't want to talk about it".

"I'm sorry".

He shook his head and said "it wasn't your fault".

"I should have been here".

"Like I said it's in the past" he then walked past the Doctor and downstairs joined everyone else eating pizza. The Doctor heard him say "you better of saved me some" along with a laugh.

The Doctor spent a couple of more minuets in Jacks office then walked out and stood on the balcony that looked over everyone. He remembered every adventure he had with each one of them then his eyes landed on his daughters. He didn't even know that Jen was alive and hadn't spent anytime with her yet he knew she was just like River. Phoebe on the other hand was more liked him and liked getting into trouble but had Rivers beauty. Yet she had the biggest destiny he had ever heard of and yet she was still his little girl. He could still remember he first steps.

He smiled but was then pulled out of his thoughts when a hand touched him. He looked to his side and could see River smiling at him. She leaned on the rail along with him and said "penny for your thoughts".

He laughed slightly and said "I can't let any of you get hurt".

She placed her hand in his and said "we won't".

He looked at her and said "you don't know that River".

"And what you do? Doctor the universe is full of mysteries and you know it. Just believe in us this one time, believe in your family".

He narrowed his eyes and said "when did you know everything?"

She sniggered and said "I learned from the best...and this time it is you".

He placed a hand on her cheek and leaned in the kiss her. The kiss was gently but they soon pulled away when Jack shouted "we don't have any rooms here so don't even think about it" they looked down and could see everyone staring at them.

They both laughed but when River started to make her way back down stairs the Doctor pulled her back and said "I love you".

She smiled and said "I love you too".

That night they all slept on camper beds at torchwood as they wanted to get away from the TARDIS noise. The Doctor woke up in the middle of the night and put his jacket on. He kissed Jen's forehead and said "I love you" he then moved on to Phoebe and as he kissed her forehead said "never be afraid, I will always be with you. I love you". He then walked over to a sleeping River where he just slept and placed a letter beside her that he wrote in Jack's office. He gentle placed his fingertips on her jaw and glided them around. He smiled and said "I promise I'll make this right. I will protect this family" he kissed her forehead and then walked towards the TARDIS.

Just as he was about to walk in River stood up and said "where do you think your going?"

"How did you-" she interrupted.

"The look in your eyes when you told me you love me. I only ever see that look when you are planning something and you don't think your going to come back" tears started to swell up and then she shouted "your not going".

Everyone started to wake up and asked what was going on. The Doctor looked River in the eye and said "I have to do this, I'm sorry".

He then ran into the TARDIS and locked the door. She banged on the door and shouted Doctor but neither him or the TARDIS would open. The Doctor stood on the opposite side of the door and as the TARDIS made a noise he said "I know girl, but it's the right thing to do" he then flew away.

At Torchwood everyone looked at River but she moved past them and grabbed the letter from the bed. It said:

_Dear everyone_

_I know you're all probably panicking right now but just think of this as ever other time I've left but I won't be returning. Kovarian will leave you all alone if she has me so it ends here. You were all amazing every single one of you. Remember the times when we fought the darleks, the cibermen and ever other alien. Just remember the times we had._

_To my family. Rory you must understand that although you told me never to break Rivers heart this was the only way she won't be in danger. I can't stand over her grave and if we ever meet again I really hope you don't use your sword. To Amy the girl who waited, you don't have you imaginary friend anymore but you have an even bigger family now. Please forgive me for what I'm doing. To Jen I know that we only just reunited but I feel like I have known you as long as Phoebe. You will always be my daughter. To Phoebe you mustn't be afraid of your destiny. You are mine and yours mothers daughter and with our combined strength and courage you will defeat it. Jenny, Phoebe please look after your mother I have a feeling that she'll listen to you two, even if it comes to having an adventure. To my darling wife River...I'm pretty sure you caught me on your way out and if you didn't I love you with all my heart. You would be suspicious to say the least as you always could figure out what I was planning, you have your mother's brains. I know we aren't the normal couple but who likes normal; we certainly don't. I told you once that I would protect this family and if that means I die at the hands of Kovarian then so be it. I love you all, please forgive me._

_Love from The Doctor_

River looked up form the letter then said "he's gone to Kovarian".

**AN: Sorry for the late update. This story only has a few more chapters left so please keep on reading.**__


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